1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified January 22, 2020
7
8Description:  Splits a file of various rRNAs into one file per type
9(16S, 18S, 5S, 23s).
10
11Usage:  splitribo.sh in=<file,file> out=<pattern>
12
13Standard parameters:
14in=<file>       Input file.
15out=<pattern>   Output file pattern, such as out_#.fa.  The # symbol is
16                required and will be substituted by the type name, such as
17                16S, to make out_16S.fa, for example.
18overwrite=f     (ow) Set to false to force the program to abort rather than
19                overwrite an existing file.
20ziplevel=9      (zl) Set to 1 (lowest) through 9 (max) to change compression
21                level; lower compression is faster.
22
23types=16S,18S,5S,23S,m16S,m18S,p16S
24                Align to these sequences.  Fewer types is faster.  m16S
25                and m18S are mitochondrial; p16S is plastid (chloroplast).
26
27Processing parameters:
28minid=0.59      Ignore alignments with identity lower than this to a
29                consensus sequences.
30refineid=0.70   Refine score by aligning to clade-specific consensus if
31                the best alignment to a universal consensus is below this.
32
33Java Parameters:
34-Xmx            This will set Java's memory usage, overriding autodetection.
35                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
36                specify 200 megs. The max is typically 85% of physical memory.
37-eoom           This flag will cause the process to exit if an out-of-memory
38                exception occurs.  Requires Java 8u92+.
39-da             Disable assertions.
40
41Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
42"
43}
44
45#This block allows symlinked shellscripts to correctly set classpath.
46pushd . > /dev/null
47DIR="${BASH_SOURCE[0]}"
48while [ -h "$DIR" ]; do
49  cd "$(dirname "$DIR")"
50  DIR="$(readlink "$(basename "$DIR")")"
51done
52cd "$(dirname "$DIR")"
53DIR="$(pwd)/"
54popd > /dev/null
55
56#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
57CP="$DIR""current/"
58
59z="-Xmx4g"
60z2="-Xms4g"
61set=0
62
63if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
64	usage
65	exit
66fi
67
68calcXmx () {
69	source "$DIR""/calcmem.sh"
70	setEnvironment
71	parseXmx "$@"
72	if [[ $set == 1 ]]; then
73		return
74	fi
75	freeRam 4000m 42
76	z="-Xmx${RAM}m"
77	z2="-Xms${RAM}m"
78}
79calcXmx "$@"
80
81mergeribo() {
82	local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@"
83	echo $CMD >&2
84	eval $CMD
85}
86
87mergeribo "$@"
88